1. Chapter 13 DNA STRUCTURE AND FUNCTION

2. Identification of Genetic material 1869, Friedrich Miescher- discovered- acidic substance (nitrogen and phosphorus) in nuclei. 1909, Archibald Garrod – “inborn errors of metabolism”- lack of enzymes. 1928, Frederick Griffith- contributed first step in identifying DNA as genetic material.

3. Identification of the Genetic Material Griffith’s Experiment

4. Avery, MacLeod and McCarty- confirmed that DNA transformed the bacteria. Isolated DNA from from heat-killed type S and injecting it along with type R bacteria into mice. The mice died and their bodies contained active type S bacteria. DNA – transforming principle

5. Conclusion DNA from type S bacteria altered the type R bacteria, enabling them to manufacture the smooth coat necessary to cause infection

6. Hershey-Chase Experiment E. coli a bacterium and T4, a virus that infects bacteria ( bacteriophage) To know which part of virus controls reproduction (replication for viruses) – the DNA or the protein coat.

7. Hershey-Chase Experiment

8. A. DNA Structure DNA is a nucleic acid composed of nucleotide monomers. DNA nucleotide consists of: one phosphate group one deoxyribose sugar (5 carbon sugar) one nitrogenous base (G, A, C or T)

9. DNA is a double-stranded helix (Watson & Crick 1953). Sides of ladder make up sugar- phosphate “backbone”. Rungs of ladder composed of base pairs joined by hydrogen bonds.

10. Pyrimidines (T & C) form hydrogen bonds with purines (A & G). Thymine pairs with Adenine, forming 2 hydrogen bonds. Cytosine pairs with Guanine, forming 3 hydrogen bonds.

11. DNA strands are antiparallel. 5’ to 3’ strand 3’ to 5’ strand Numbering of strands is based on position of deoxyribose sugars.

12. DNA is highly condensed. DNA is wrapped tightly around proteins & folded. DNA must unwind for replication to occur.

13. The DNA molecule is a double helix with sugar-phosphate rails and pyrimidine-purine pairs as rungs. The strands run antiparallel to one another as the 5’ to 3’ direction. DNA is very highly packaged to fit into the nucleus. Cells use specific proteins called histones to package and organize the DNA within the nucleus.

14. B. DNA Replication Process by which DNA is duplicated. occurs during the S phase of Interphase is semiconservative (Meselson & Stahl)

15. Overview of DNA Replication:  Unreplicated DNA.  Strands “unzip” at several points creating replication forks.  Each strand serves as template for complementary nucleotides to H-bond.  New nucleotides of each daughter strand are linked.

16. Steps in DNA Replication:  Helicase breaks hydrogen bonds.  Binding proteins stabilize strands; prevent them from rejoining.  Primase makes an RNA primer.

17.  Free nucleotides move in & H-bond; DNA polymerase links nucleotides to each other starting at primer & working in the 5’ to 3’ direction.  DNA polymerase “proofreads” new strand (replaces incorrect bases).

18.  DNA replication is continuous on one strand.  DNA replication is discontinuous on other strand, producing Okazaki fragments.

19.  Repair enzymes remove RNA primers; Ligase connects Okazaki fragments. Ligase

20. Determine the base sequence of daughter DNA replicated from the following parental DNA strand. parental DNA C T A G G T A C T daughter DNA G A T C C A T G A

21. DNA replication makes use of enzymes to accurately copy the information. The two strands- separated by helicase; primase then builds a short piece of RNA to which DNA polymerase add DNA nucleotides as it builds the new strands. Ligase seals two adjacent pieces together. A different form of DNA polymerase removes RNA and incorrect bases. Replication begins at hundreds of origins of replication to rapidly duplicate the entire DNA in most cells.

22. C. DNA Repair UV radiation damages DNA by causing thymine dimers to form. DNA damage can be repaired by photoreactivation or excision repair.

23. 1. Photoreactivation – photolyase (enzyme) uses light energy to split dimer. 2. Excision repair - repair enzyme cuts out damaged area; DNA polymerase inserts replacement sequence & ligase seals backbone.

24. 3. Mismatch repair - enzymes proofread newly replicated DNA for base mispairing & correct the error. Faulty DNA repair results in chromosome breaks & an increased susceptibility to cancer. Ex. Xeroderma pigmentosum

25. D. Comparison of DNA & RNA

26. DNA to RNA to Protein

27. E. Transcription Process by which a molecule of RNA is synthesized that is complementary to a specific sequence of DNA Occurs in the nucleus of eukaryotic cells & cytoplasm of prokaryotic cells. Is regulated by operons (bacterial cells) or transcription factors (multicellular organisms). Involves 3 stages: initiation, elongation & termination

28. Operons turn genes on or off in Bacteria

29. To conserve energy, cells control which proteins are made in response to need by controlling transcription. Ex. Lactose operon which prevents transcription of a set of genes needed for lactose utilization in the absence of lactose. Proteins act like molecular switches that “sense” the presence of other molecules and signals. Mechanisms exist in higher organisms to control gene expression that use transcription factors to activate RNA polymerase.

30. 1. Initiation RNA polymerase attaches to a promoter on DNA strand. Helicase unzips a short section of DNA. Free RNA nucleotides move in & H-bond to complementary bases on DNA template strand.

31. 2. Elongation RNA polymerase links RNA nucleotides together in a 5’ to 3’ direction. Growing RNA strand peels away from DNA template. 3. Termination RNA polymerase detaches when it reaches a terminator. Completed RNA molecule is released from DNA template.

32. Usually, several copies of RNA are made at a time. Determine the base sequence of RNA transcribed from the following DNA template strand. DNA template C A G T A A G C C RNA strand G U C A U U C G G 123

33. Three major types of RNA are transcribed. mRNA (messenger RNA) - encodes genetic information from DNA & carries it into the cytoplasm. Each three consecutive mRNA bases forms a genetic code word (codon) that codes for a particular amino acid. codon 5’3’

34. rRNA (ribosomal RNA) - associates with proteins to form ribosomes. Subunits are separate in the cytoplasm, but join during protein synthesis (translation). large subunit small subunit

35. tRNA (transfer RNA) - transports specific amino acids to ribosome during protein synthesis (translation). Anticodon - specific sequence of 3 nucleotides; complementary to an mRNA codon. Amino acid accepting end Anticodon sequence determines the specific amino acid that binds to tRNA.

36. Eukaryotic mRNA must be processed before it exits nucleus & enters cytoplasm. nucleotide cap is added “poly A tail” is added introns are removed

37. RNA – multifunctional molecule- participates in protein synthesis Messenger RNA carries a gene’s sequence information Ribosomal RNA - part of ribosomes- support and bring together amino acids as protein form Transfer RNA - matches specific amino acids to specific mRNA triplets, enabling ribosomes to assemble proteins. In eukaryotic cells introns removed from mRNA before translation to produce complete gene sequence of exons.

38. F. Translation Process by which an mRNA sequence is translated into an amino acid sequence (polypeptide/protein). Occurs in the cytoplasm of eukaryotic & prokaryotic cells. Requires: mRNA, tRNAs, amino acids & ribosomes. Involves 3 stages: initiation, elongation & termination

39. The Genetic Code

40. 1. Initiation Small ribosomal subunit binds to “start codon” [AUG] on mRNA molecule. AUG codon attracts initiator tRNA.

41. 2. Elongation Large ribosomal subunit binds to small subunit. A second tRNA anticodon binds to the next mRNA codon. A peptide bond forms between the two amino acids.

42. Initiator tRNA is released. Ribosome moves down mRNA by 1 codon. A third tRNA anticodon binds to the next mRNA codon. A peptide bond forms between 2nd & 3rd amino acids.

43. tRNAs continue to add amino acids; polypeptide lengthens.

44. 3. Termination Occurs when ribosome reaches an mRNA stop codon (UGA, UAG or UAA). Stop codons do NOT specify an amino acid. Last tRNA is released, ribosomal subunits separate & new polypeptide/protein is released.

45. Usually, several copies of the polypeptide/protein are made at a time. Some polypeptides must be altered before they can function. 123456

46. Determine the amino acid sequence a ribosome would translate from the following mRNA strand. mRNA C A U G G C U C A A U G A AlaGlnSTOPMet

47. Review: Genetic information flows in cell from DNA  RNA  protein. Each gene on DNA codes for production of a specific polypeptide/amino acid.

48. Genetic code – correspondence between genetic instructions in mRNA and amino acids. Each codon corresponds to a single amino acid. All the organisms use the same genetic code with a few rare exceptions in mitochondria.

49. Ribosomes align codons and amino acids and then bind the amino acids together as a polypeptide. Chaperones and other proteins help fold the protein into its final conformation, which is dictated by the amino acid sequence itself.

50. G. Mutation A physical change in the nucleotide sequence of DNA. May not affect phenotype (silent mutation). Can affect somatic cells (somatic mutation) or sex cells (germinal mutation). Can form spontaneously or be induced by a mutagen.

51. 1. Point mutation - one DNA nucleotide replaces another missense mutation - point mutation that changes a codon to specify a different amino acid. Ex. sickle cell disease

52. nonsense mutation - point mutation that changes an amino acid-specifying codon into a stop codon. 2. Frameshift mutation - the insertion or deletion of DNA nucleotides; results in disruption of the reading frame. Ex. cystic fibrosis 3. Expanding repeat - the # of copies of a 3 or 4 nucleotide sequence increases over several generations. Ex. myotonic dystrophy

54. Natural protection against mutation DNA proofreading DNA repair checking RNAs as they are made eliminating malformed proteins genetic code

55. Protection in genetic code: synonymous codons encode same amino acid, 3 rd position differs mutation in 2 nd codon position changes specification to similar amino acid mutation affects phenotype only if it alters protein’s function

56. Mutations- changes in the genetic instructions within a gene. Single changes in bases- point mutation- can be invisible or produce tremendous changes in the resulting protein. Frameshift mutation often terminate the protein early, resulting in loss of function for the cell. Other point mutations- cause life’s diversity. Radiations and chemicals are common mutagens. Most mutations occur spontaneously through replication errors.